R/sitedis.R

In drmarcogir/Rmacdiv:

#' Dissimilarity between sites
#'
#' @ inrast = environmental raster
#' @ plotdf = site info dataframe
#'
#'

sitedis<-function(inrast){
  # extract environmental information from sites
  as.data.frame(siteinfo) %>%
    dplyr::select(Database.code,Islandnew) %>%
    mutate(variable=raster::extract(inrast,siteinfo)) ->tmp
  # create dissimilarity (distance matrix)
  isl.l<-as.character(unique(tmp$Islandnew))
  results<-NULL
  for (y in 1: length(isl.l)){
    # subset site info for a given Island
    islinfo<-subset(decayinfo1,Island==isl.l[y])
    # subset environmental info for a given island
    envinfo<-subset(tmp,Islandnew==isl.l[y])
    # goes through each row
    for (i in 1:dim(islinfo)[1]){
      difference<-dplyr::filter(envinfo,Database.code==islinfo[i,]$NBX)$variable-dplyr::filter(envinfo,Database.code==islinfo[i,]$NBY)$variable
      resdf<-data.frame(islinfo[i,][1:3],envdif=difference)
      results<-rbind(results,resdf)
    }
  }
  return(results)
}